--- Makefile.orig	2018-05-09 00:33:23 UTC
+++ Makefile
@@ -1,7 +1,8 @@
-OPTFLAG = -O3
-INCLUDES = -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2
-CXXFLAGS = -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS
-CXX = g++
+# ${LOCALBASE}/include must come after bundled dirs
+INCLUDES = -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I${LOCALBASE}/include
+CXXFLAGS ?= -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS
+CXXFLAGS += -std=c++0x $(INCLUDES) -D__STDC_LIMIT_MACROS
+CXX ?= g++
 
 SOURCESONLY =
 
@@ -139,11 +140,11 @@ SOURCESONLY = main.cpp
 TARGET = vt
 TOOLSRC = $(SOURCES:=.cpp) $(SOURCESONLY)
 TOOLOBJ = $(TOOLSRC:.cpp=.o)
-LIBDEFLATE = lib/libdeflate/libdeflate.a
-LIBHTS = lib/htslib/libhts.a
+LIBDEFLATE = -ldeflate
+LIBHTS = -lhts
 LIBRMATH = lib/Rmath/libRmath.a
 LIBPCRE2 = lib/pcre2/libpcre2.a
-LIBSVM = lib/libsvm/libsvm.a
+LIBSVM = -lsvm
 
 all : $(TARGET)
 
@@ -165,8 +166,8 @@ ${LIBSVM} :
 version :
 	git rev-parse HEAD | cut -c 1-8 | awk '{print "#define VERSION \"0.5772-"$$0"\""}' > version.h;
 
-$(TARGET) : ${LIBHTS} ${LIBRMATH} ${LIBPCRE2}  ${LIBSVM} $(TOOLOBJ) 
-	$(CXX) $(CXXFLAGS) -o $@ $(TOOLOBJ) $(LIBHTS) $(LIBRMATH) ${LIBPCRE2} ${LIBDEFLATE} -lz -lpthread -lbz2 -llzma -lcurl -lcrypto
+$(TARGET) : ${LIBRMATH} ${LIBPCRE2} $(TOOLOBJ) 
+	$(CXX) $(CXXFLAGS) -o $@ $(TOOLOBJ) -L${LOCALBASE}/lib $(LIBHTS) $(LIBRMATH) ${LIBPCRE2} ${LIBDEFLATE} -lz -lpthread -lbz2 -llzma -lcurl -lcrypto
 
 $(TOOLOBJ): $(HEADERSONLY)